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AllelicImbalance (version 1.6.2)
Investigates allele specific expression
Description
Provides a framework for allelic specific expression investigation using RNA-seq data.
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1.10.2
1.8.3
1.6.2
1.4.2
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Version
1.6.2
License
GPL-3
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Repository
https://github.com/pappewaio/AllelicImbalance
Maintainer
Jesper R Gadin
Last Published
May 16th, 2015
Functions in AllelicImbalance (1.6.2)
Search functions
ASEset-class
ASEset objects
ASEset.sim
ASEset.sim object
ASEset-gbarplot
gbarplot ASEset objects
ASEset-scanForHeterozygotes
scanForHeterozygotes
ASEsetFromBam
ASEset from bam file
annotationBarplot
add annotation to AllelicImbalance barplot
ASEset-barplot
barplot ASEset objects
ASEset-glocationplot
glocationplot ASEset objects
AllelicImbalance-package
A package meant to provide all basic functions for high-throughput allele specific expression analysis
ASEset-gviztrack
ASEset-gviztrack ASEset objects
cigar-utilities
realCigarPosition
boxplot
boxplots
countAllelesFromBam
alleleCounts from bam file
chisq.test
chi-square test
binom.test
binomial test
barplot-lattice-support
lattice barplot inner functions for ASEset objects
decorateWithGenes
decorateWithGenes
defaultMapBias
Generate default mapbias from genotype
coverageMatrixListFromGAL
coverage matrix of GAlignmentsList
decorateWithExons
decorateWithExons
DetectedAI-class
DetectedAI class
genofilters
genotype filter methods
fractionPlotDf
Plot Dataframe
defaultPhase
defaultPhase
getAlleleCounts
snp count data
getSnpIdFromLocation
Get rsIDs from locations of SNP
gba
global analysis wrapper
detectAI
detectAI
getDefaultMapBiasExpMean
Map Bias
getAreaFromGeneNames
Get Gene Area
import-bam-2
Import Bam-2
import-bcf
Import Bcf Selection
import-bam
Import Bam
GRvariants
GRvariants object
implodeList.old
implode list of arguments into environment
inferGenotypes
infererence of genotypes from ASEset count data
GlobalAnalysis-class
GlobalAnalysis class
histplot
histogram plots
inferAltAllele
inferAltAllele
inferAlleles
inference of SNPs of ASEset
phaseArray2Matrix
phaseArray2Matrix
phaseMatrix2Array
phaseMatrix2Array
initialize-DetectedAI
Initialize DetectedAI
makeMaskedFasta
makes masked fasta reference
initialize-ReferenceBias
Initialize ReferenceBias
initialize-ASEset
Initialize ASEset
legendBarplot
add legend to AllelicImbalance barplot
ASEset-locationplot
locationplot ASEset objects
mapBiasRef
mapBias for reference allele
initialize-GlobalAnalysis
Initialize GlobalAnalysis
reads
reads object
randomRef
Random ref allele from genotype
regionSummary
regionSummary
refAllele
Reference allele
ReferenceBias-class
ReferenceBias class
scanForHeterozygotes.old
scanForHeterozygotes-old
ReferenceBias-show
genotype filter methods
refFraction
reference fraction